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- PDB-5v7z: SSNMR Structure of the Human RIP1/RIP3 Necrosome -

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Basic information

Entry
Database: PDB / ID: 5v7z
TitleSSNMR Structure of the Human RIP1/RIP3 Necrosome
Components
  • PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
  • THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
KeywordsSIGNALING PROTEIN / signaling complex / human functional amyloid
Function / homology
Function and homology information


regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / ripoptosome assembly / positive regulation of miRNA processing / regulation of adaptive immune response / positive regulation of interleukin-6-mediated signaling pathway / execution phase of necroptosis / death domain binding / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / ripoptosome assembly / positive regulation of miRNA processing / regulation of adaptive immune response / positive regulation of interleukin-6-mediated signaling pathway / execution phase of necroptosis / death domain binding / regulation of T cell mediated cytotoxicity / regulation of activated T cell proliferation / ripoptosome assembly involved in necroptotic process / T cell apoptotic process / programmed necrotic cell death / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / regulation of type II interferon production / activation of protein kinase activity / positive regulation of macrophage differentiation / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / necroptotic process / negative regulation of necroptotic process / JUN kinase kinase kinase activity / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / spleen development / RIP-mediated NFkB activation via ZBP1 / death-inducing signaling complex / positive regulation of necroptotic process / Dengue virus modulates apoptosis / T cell homeostasis / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / lymph node development / positive regulation of programmed necrotic cell death / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / positive regulation of programmed cell death / extrinsic apoptotic signaling pathway via death domain receptors / thymus development / TRP channels / protein serine/threonine phosphatase activity / response to tumor necrosis factor / T cell differentiation in thymus / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway / canonical NF-kappaB signal transduction / signaling adaptor activity / apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / TICAM1, RIP1-mediated IKK complex recruitment / protein serine/threonine kinase binding / IKK complex recruitment mediated by RIP1 / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to tumor necrosis factor / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / positive regulation of JNK cascade / cellular response to hydrogen peroxide / Regulation of necroptotic cell death / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / response to oxidative stress / defense response to virus / amyloid fibril formation / Potential therapeutics for SARS / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / non-specific serine/threonine protein kinase / signaling receptor complex / transcription coactivator activity / endosome membrane / intracellular signal transduction / Ub-specific processing proteases / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression
Similarity search - Function
RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase ...RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 1 / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics / molecular dynamics
AuthorsMompean, M. / Li, W. / Li, J. / Laage, S. / Siemer, A.B. / Wu, H. / McDermott, A.E.
CitationJournal: Cell / Year: 2018
Title: The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex.
Authors: Mompean, M. / Li, W. / Li, J. / Laage, S. / Siemer, A.B. / Bozkurt, G. / Wu, H. / McDermott, A.E.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
B: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
C: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
D: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
E: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
F: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE
G: PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP
H: THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE


Theoretical massNumber of molelcules
Total (without water)14,5168
Polymers14,5168
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9690 Å2
ΔGint-48 kcal/mol
Surface area8380 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1target function

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Components

#1: Protein/peptide
PRO-LEU-VAL-ASN-ILE-TYR-ASN-CYS-SER-GLY-VAL-GLN-VAL-GLY-ASP


Mass: 1577.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y572*PLUS
#2: Protein/peptide
THR-ILE-TYR-ASN-SER-THR-GLY-ILE-GLN-ILE-GLY-ALA-TYR-ASN-TYR-MET-GLU-ILE


Mass: 2051.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13546*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1DARR 250 MS
122isotropic1DARR 250 MS
133isotropic1DARR 250 MS
141isotropic2CHHC 500 US
153isotropic2CHHC 500 US
162isotropic2PAR 15 MS
173isotropic2PAR 15 MS
182isotropic2PAIN 6 MS
193isotropic2PAIN 6 MS
1101isotropic2TEDOR 8 MS
1112isotropic2TEDOR 8 MS
1123isotropic2TEDOR 8 MS
1131isotropic2NCOCX
1141isotropic2NCOCA
1151isotropic2NCACX
1161isotropic2NCA
1171isotropic1DARR 50 MS
1182isotropic1DARR 50 MS
1193isotropic1DARR 50 MS
1201isotropic1DARR 20 MS
1212isotropic1DARR 20 MS
1223isotropic1DARR 20 MS
1231isotropic1DARR 100 MS
1242isotropic1DARR 100 MS
1253isotropic1DARR 100 MS
1261isotropic1DARR 500 MS
1272isotropic1DARR 500 MS
1283isotropic1DARR 500 MS

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
fiber115 mg/mL [U-100% 13C; U-100% 15N] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
fiber215 mg/mL [U-100% 15N; 2-13C-GLYCEROL] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
fiber315 mg/mL [U-100% 15N; 1,3-13C-GLYCEROL] RIP1/RIP3, 100% H2OFIBRIL_SAMPLE100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
15 mg/mLRIP1/RIP3[U-100% 13C; U-100% 15N]1
15 mg/mLRIP1/RIP3[U-100% 15N; 2-13C-GLYCEROL]2
15 mg/mLRIP1/RIP3[U-100% 15N; 1,3-13C-GLYCEROL]3
Sample conditionsIonic strength: 0 Not defined / Label: CONDITIONS_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9001
Bruker AVANCEBrukerAVANCE7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
torsion angle dynamics1
molecular dynamics2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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